Scientists Develop Water-Soluble Nanoarray for RNA

Scientists at Arizona State University say that they have developed a gene detection platform made up entirely from self-assembled DNA nanostructures.

A recent breakthrough of making spatially addressable DNA nanoarrays came from work on scaffolded DNA origami. In this method, a long single-stranded viral DNA scaffold can be folded and stapled by a large number of short synthetic helper strands into nanostructures that display complex patterns.

“But, the potential of structural DNA nanotechnology in biological applications has been underestimated, and if we look at the process of DNA self-assembly, you will be amazed that trillions of DNA nanostructures can form simultaneously in a solution of few microliters, and very importantly, they are biocompatible and water soluble,” says Hao Yan, Ph.D., a member of the university’s Center for Single Molecule Biophysics and an assistant professor of chemistry and biochemistry.

“In this work, we developed a water soluble nanoarray that can take advantage of the DNA self-assembling process and also have benefits that the macroscopic DNA microchip arrays do not have,” Dr. Yan adds. “The arrays themselves are reagents, instead of solid surface chips.”

To make the DNA origami RNA probes, the investigators took advantage of the basic DNA pairing rules. By controlling the exact position and location of the chemical bases within a synthetic replica of DNA, Dr. Yan programmed a single stranded genomic DNA, M13, into nanotiles to contain the probes for specific gene expression targets. In a single step, the M13 scaffold system can churn out as many as 100 trillion of the tiles with close to 100% yield, according to Dr. Yan.

The research team designed three different DNA probe tiles to detect three different RNA genes along with a bar code index to tell the tiles apart from each other. The group used atomic force microscopy (AFM) to image the tiles at the single molecule level.

“Each probe actually contains two half probes, so when the target RNA comes in, it will hybridize to the half probes and turn the single stranded dangling probes into a stiff structure,” explains Dr. Yan. “When it is stiffened, it will be sensed by the atomic force microscope cantilever, and you can see a bright line, which is a height increase. The result is a mechanical, label-free detection.

“Since the DNA-RNA hybridization has such a strong affinity,” notes Dr. Yan, “in principle, a single molecule would be able to hybridize to the probe tile.”